Contacts of the strand formed by residues 178 - 184 (chain A) in PDB entry 2JGB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PRO 6.4 0.2 - - - -
105A GLY* 5.3 5.5 - - - -
138A ARG* 3.6 0.3 - - - -
139A LEU* 2.8 38.8 + - + +
140A ARG 4.6 0.5 - - - +
141A LYS* 2.6 48.3 + - - +
142A GLY 4.4 3.5 + - - -
144A ALA* 3.5 35.1 + - + +
171A VAL* 5.2 0.4 - - + -
172A SER 3.2 9.6 - - - +
173A VAL* 3.1 17.6 - - - +
177A GLU* 1.3 75.8 - - - +
179A ILE* 1.3 70.4 + - - +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 3.9 21.1 - - + -
137A ILE 3.3 12.3 - - - +
138A ARG* 4.2 15.3 - - + +
170A VAL 3.9 0.5 - - - +
171A VAL* 3.4 3.0 - - - +
172A SER* 2.8 50.2 + - - +
174A ARG* 3.7 28.7 - - + +
177A GLU* 3.5 25.6 - - + +
178A ASP* 1.3 81.0 - - - +
180A ILE* 1.3 68.4 + - - +
181A SER* 3.9 17.6 + - - +
234A PHE* 4.1 7.9 - - + -
1000B MGT 5.9 0.2 - - - +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP 3.9 0.3 - - - +
136A ILE* 3.4 0.5 - - - -
137A ILE* 2.8 59.6 + - + +
139A LEU* 4.0 17.5 - - + +
144A ALA* 4.7 5.8 - - + +
147A CYS* 3.8 26.2 - - + -
148A TRP* 4.7 7.6 - - + +
151A LEU* 4.5 13.2 - - + -
170A VAL 3.4 4.0 - - - +
171A VAL* 3.8 23.8 - - + -
179A ILE* 1.3 77.5 - - - +
181A SER* 1.3 63.7 + - - +
204A LEU* 3.5 32.5 - - + -
206A LEU* 5.1 0.2 - - + -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 4.2 6.0 + - - +
135A TRP 3.1 10.5 - - - -
136A ILE* 3.3 22.5 - - - +
151A LEU* 3.7 5.6 - - - +
169A ALA* 3.2 7.6 - - - +
170A VAL* 2.9 40.1 + - - +
172A SER* 5.4 1.7 + - - -
179A ILE* 3.9 7.8 + - - +
180A ILE* 1.3 77.0 + - - +
182A ILE* 1.3 62.3 + - - +
183A TRP* 4.1 20.2 - - - -
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 3.1 2.9 - - - -
135A TRP* 3.0 36.5 + - + +
151A LEU* 4.0 13.0 - - + -
155A MET* 4.8 5.4 - - - -
160A PHE* 3.3 40.4 - - + -
166A ILE* 4.0 22.7 - - + -
168A GLY 3.5 14.1 - - - +
169A ALA* 4.8 1.3 - - + -
181A SER* 1.3 76.2 - - - +
183A TRP* 1.3 70.3 + - - +
184A ASN* 4.2 1.4 + - - +
196A ILE* 3.6 24.3 - - + +
200A LEU* 3.8 22.2 - - + -
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Residues in contact with TRP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 6.2 0.2 - - - -
116A PHE* 3.6 21.5 - + + -
122A PRO 3.8 18.4 - - - -
123A MET 3.8 13.5 - - - -
124A TRP* 3.8 20.6 - + - -
129A ASN* 3.7 30.7 - - - +
133A GLY 3.3 5.8 - - - +
134A LYS* 3.6 28.5 - - + +
166A ILE* 3.8 4.9 - - - +
167A CYS* 2.8 32.8 + - + -
168A GLY 2.9 14.7 + - - +
170A VAL* 3.8 20.0 - - + +
181A SER* 4.1 7.2 - - - -
182A ILE* 1.3 84.1 - - - +
184A ASN* 1.3 60.9 + - - +
196A ILE* 5.7 0.2 - - - -
217A HIS* 3.4 28.0 - + - +
1000B MGT 3.9 17.0 - - - -
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Residues in contact with ASN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA 4.9 0.2 - - - +
129A ASN* 5.0 1.0 - - - +
132A GLY* 3.2 2.6 - - - -
133A GLY 2.9 30.6 + - - +
134A LYS* 5.0 0.3 - - - -
135A TRP* 5.4 0.3 - - - -
165A GLU* 3.0 37.1 + - - +
166A ILE* 4.6 0.4 - - - -
167A CYS* 3.7 7.2 - - - -
182A ILE 4.2 0.9 + - - +
183A TRP* 1.3 74.2 - - - +
185A LYS* 1.3 61.7 + - - +
186A THR 3.1 22.2 + - - +
192A THR* 3.8 10.5 - - - +
193A THR* 3.9 4.2 - - - +
196A ILE* 3.7 27.3 - - + +
214A TYR* 2.7 31.1 + - - -
217A HIS* 4.7 2.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il